User:Tom Gluick/glutamine synthetase/Assignment 1

The Assignment: My Intent
'''Assignment 1: IIA. Quaternary Structure:' Provide an overview of the quaternary structure of Salmonella typhimurium''  Glutamine Synthetase. Your explanation ought to include stoichiometry, how the monomers are joined to from the quaternary structure, a clever way to show the symmetry, an indication of the active site location.

My Hope and Intent: I hoped that the students would choose a subunit and show the quaternary contacts by showing the surfaces that interacted between the subunits one by one. They would then comment on the interaction in some fashion. I hoped the students would be able to devise a way to show symmetry. i hoped the students would show the location of the active site.

Student Contribution
 Quarternary Structure 

The enzyme Glutamine Synthetase is made up of twelve subunits. The structure consists of two identical hexameric rings held together by hydrophobic and hydrogen bonding forces. The N-terminal helix of each subunit is exposed to hydrophilic solvent, where as the C-terminal is enshrouded in hydrophobic regions within the helical structure of the rings. The central channel is linked together by six four-stranded anti-parallel L-sheets which along with the twelve monomers enhance the stability of the protein structure.

 Quarternary Interactions 

The subunits are connected through couple of different type of interactions, such as: Hydrogen Bonds, and Non-bonded contacts. Each subunit has area’s that are proportional to the surface area of the corresponding protein chains. Each subunit only interacts with four other protomers in the protein.

Subunit Connections:

Glutamine Synthetase with interactions between all residues

Interactions with Chain A

A interacts with four subunits, F, G, H, and B.

Interactions with Chain B

B interacts with four subunits, H, I, A, and C.

Interactions with Chain C

C interacts with four subunits, B, D, I, and J.

Interactions with Chain D

D interacts with four subunits, C, I, J, and K.

Interactions with Chain E

E interacts with four subunits, L, F, D, and K.

Interactions with Chain F

F interacts with four subunits, A, G, L, and E.

Interactions with Chain G

G interacts with four subunits, A, H, L, and F.

Interactions with Chain H

H interacts with four subunits, A, B, G, and L.

Interactions with Chain I

I interacts with four subunits, B, H, C, and J.

Interactions with Chain J

J interacts with four subunits, I, C, D, and K.

Interactions with Chain K

K interacts with four subunits, E, L, J, and D.

Interactions with Chain L

L interacts with four subunits, E, F, A, and G.

Active Site Glutamine Synthetase is dodecameric and has 622 symmetry. Each active site is located at an interface between subunits, and is made up of residues from two adjacent subunits. The active site location is between two protomers and indicated by the yellow manganese atoms highlighted in the applet. The active site can be described as a 'bifunnel' in which ATP and glutamate bind at opposite ends. It is surrounded by three important ligands: ADP, TL as labeled in the applet. ADP is short for Adenosite Diphosphate. And the metal ion, Thallium is also labeled in the applet.

Reference
1. Eisenberg, David and Gill, Harindarpal and Pfluegl, Gaston and Rotstein, Sergio. “Structure-function relationships of glutamine synthetases.” Elsevier, archives of biochemistry and biophysics 1477(Dec 1999):122-123.

2. Eisenberg, Gill. "Crystal structure of glutamine synthetase from salmonella typhimurium with thallium ions" PDBsum. european bioinformatics institute 2006-2008. <http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1f1h&template=main.html>

Assessment
To complete this assignment, I asked the students to use PDBsum (one of my favorites) to assist them in their efforts to understand quaternary structure of glutamine synthetase. In PDBsum page on GS, there is a tab linking to protein-protein interactions in GS. One subunit interacts with four other subunits. Some of the subunit-subunit contacts are extensive and the others are few. I directed the students to pick one subunit and discuss how it interacts with its neighbors. The following link shows the interactions. Unfortunately, the students merely translated the PDBsum table to their user page and wrote scripts displaying each subunit clustered with four other subunits. For instance the green link: Interactions with Subunit A  would have been a great start to a discussion of quaternary structure. I hoped the students would select the residues involved in quaternary contacts and find a reasonable way to show the contacts--such as mesh with ball and stick representation. Perhaps, this is too advanced for undergraduates. I will amend the assignment (amendments shown in red on main page) to provide students with more direction; it appears that the assignment was too open ended for undergraduate students given the time to complete the assignment.

The students did make a valiant and imaginative attempt to show symmetry, but it did not really show the symmetry operation. I will remove this from this assignment and make it a separate assignment. The students indicated the active site by showing where the ligand binds, which is fine.